Shape Keys: Why did it do this?
Shape keys are for when the modeling is done. Don't start adding shape keys and then expect to be able to add verts, edges or faces later. You may still move verts around a little, but results are sometimes unpredictable.

https://blenderartists.org/forum/showthread.php?303554-Editing-the-Basis-shape-key-after-making-shapekeys

Can I fix broken shape keys after editing basis?